Custom Properties in space_data or region3d
See this answer for a listing of classes which support custom properties.
Neither Space nor RegionView3D derive from ID and are not treated special and can not have custom properties.
Screen does inherit and might be a candidate. You might identify an area by its index or its hash.
The former should work with loading/saving the screen from/to the *.blend file. 
The latter might persist during changes to the screen layout at runtime.